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List of Galaxy tools
This is a list of all of the tools that are, or have been, available on the Galaxy Project server. Get Data * Upload File from your computer * UCSC Main table browser * UCSC Archaea table browser * EBI SRA ENA SRA * BioMart Central server * GrameneMart Central server * Flymine server * modENCODE fly server * modENCODE modMine server * MouseMine server * Ratmine server * YeastMine server * modENCODE worm server * WormBase server * ZebrafishMine server * EuPathDB server * GenomeSpace import from file browser Send Data Lift-Over Text Manipulation Convert Formats Filter and Sort Join, Subtract and Group NGS: QC and manipulation * FastQC Read Quality reports * Select high quality segments * Build base quality distribution * Draw quality score boxplot * Quality format converter (ASCII-Numeric) * Filter by quality * FASTQ to FASTA converter * Remove sequencing artifacts * Barcode Splitter * Clip adapter sequences * Collapse sequences * Draw nucleotides distribution chart * Compute quality statistics * Rename sequences * Reverse-Complement * Trim sequences * Combine FASTA and QUAL into FASTQ * Filter FASTQ reads by quality score and length * Manipulate FASTQ reads on various attributes * FASTQ Groomer convert between various FASTQ quality formats * FASTQ Masker by quality score * FASTQ joiner on paired end reads * FASTQ splitter on joined paired end reads * FASTQ Summary Statistics by column * FASTQ to FASTA converter * FASTQ to Tabular converter * FASTQ Trimmer by column * FASTQ Quality Trimmer by sliding window * Tabular to FASTQ converter * Convert SOLiD output to fastq * Compute quality statistics for SOLiD data * Draw quality score boxplot for SOLiD data NGS: Mapping NGS: RNA-seq NGS: SAMtools * bcftools view Converts BCF format to VCF format * Reheader copy SAM/BAM header between datasets * Split BAM dataset on readgroups * Stats generate statistics for BAM dataset * BAM-to-SAM convert BAM to SAM * Sort BAM dataset * CalMD recalculate MD/NM tags * BedCov calculate read depth for a set of genomic intervals * IdxStats tabulate mapping statistics for BAM dataset * Flagstat tabulate descriptive stats for BAM datset * Slice BAM by genomic regions * SAM-to-BAM convert SAM to BAM * RmDup remove PCR duplicates * MPileup call variants * Pileup-to-Interval condenses pileup format into ranges of bases * Filter pileup on coverage and SNPs * Convert SAM to interval * Filter SAM on bitwise flag values * Generate pileup from BAM dataset * Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region NGS: BAM Tools NGS: Picard NGS: VCF Manipulation Extract Features Fetch Sequences Fetch Alignments Get Genomic Scores Operate on Genomic Intervals Statistics Graph/Display Data Phenotype Association snpEff BEDTools Genome Diversity EMBOSS Regional Variation FASTA manipulation Evolution Multiple Alignments Metagenomic analyses Motif Tools NGS TOOLBOX BETA NGS: Peak Calling NGS: Variant Analysis NGS: GATK Tools (beta) NGS: Picard (beta) RNA Structure Prediction External Links * Galaxy Category: Galaxy Project